Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A7 F1 I2 R1 766 64.2 3232166 90.9% 2938038 104.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,784,529 C→T pseudogene (483/1374 nt) ypjC ← pseudogene

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,784,5290CT100.0% 145.4 / NA 46pseudogene (483/1374 nt)ypjCpseudogene
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (24/22);  total (24/22)

ATCTATTTTGTTTTCATATGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTCTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGACCTGCTTG  >  NC_000913/2784394‑2784661
                                                                                                                                        |                                                                                                                                    
aTCTATTTTGTTTTCATATGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTa                                                                                                                                    >  2:654893/1‑139 (MQ=255)
aTCTATTTTGTTTTCATATGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTAt                                                                                                                                   >  2:582764/1‑139 (MQ=255)
                tatGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                                   <  1:531393/139‑1 (MQ=255)
                 atGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                                   <  1:654893/139‑1 (MQ=255)
                    aaTTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCa                                                                                                                                <  1:1159005/122‑1 (MQ=255)
                    aaTTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCa                                                                                                                                >  2:1159005/1‑122 (MQ=255)
                             aTTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCAt                                                                                                                               <  1:758091/114‑1 (MQ=255)
                             aTTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCAt                                                                                                                               >  2:758091/1‑114 (MQ=255)
                              ttCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                                   >  2:86181/1‑125 (MQ=255)
                              ttCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                                   <  1:86181/125‑1 (MQ=255)
                              ttCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGa                                                                                                     >  1:445114/1‑139 (MQ=255)
                               tCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGAt                                                                                                    <  2:873793/139‑1 (MQ=255)
                                   tACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                                   <  1:271384/120‑1 (MQ=255)
                                   tACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                                   >  2:271384/1‑120 (MQ=255)
                                   tACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                                   >  2:1154941/1‑120 (MQ=255)
                                   tACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                                   <  1:1154941/120‑1 (MQ=255)
                                        aCATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCAt                                                                                                                               >  2:203531/1‑103 (MQ=255)
                                        aCATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCAt                                                                                                                               <  1:203531/103‑1 (MQ=255)
                                        aCATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCa                                                                                               >  1:1009679/1‑135 (MQ=255)
                                        aCATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCa                                                                                               <  2:1009679/135‑1 (MQ=255)
                                             tGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgtgc                                                                                                                   <  1:761316/110‑1 (MQ=255)
                                             tGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                                   >  2:761316/1‑110 (MQ=255)
                                             tGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTa                                                                                      >  2:72304/1‑139 (MQ=255)
                                                              tAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGt                                                                     <  1:72304/139‑1 (MQ=255)
                                                                        cgTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAac                                                           >  1:107079/1‑139 (MQ=255)
                                                                           actactTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAAcaca                                                        >  2:663838/1‑139 (MQ=255)
                                                                               ctTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                                   <  1:182520/76‑1 (MQ=255)
                                                                               ctTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                                   >  2:182520/1‑76 (MQ=255)
                                                                               ctTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCat                                                                                              >  2:591433/1‑97 (MQ=255)
                                                                               ctTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCat                                                                                              <  1:591433/97‑1 (MQ=255)
                                                                                   gCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCAtt                                                >  2:1507180/1‑139 (MQ=255)
                                                                                    cTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCGAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGtt                                                                    <  2:1053386/118‑1 (MQ=255)
                                                                                    cTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCATTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGtt                                                                    >  1:1053386/1‑118 (MQ=255)
                                                                                             a‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCAt                                                                                                                               >  2:753544/1‑50 (MQ=255)
                                                                                             a‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCAt                                                                                                                               <  1:753544/50‑1 (MQ=255)
                                                                                               ccAACATGAACATCACTTTTTCTTATATTATCGAAAAAGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGcc                                     <  1:1075795/139‑2 (MQ=255)
                                                                                                                       atatTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGtttt                                           <  2:1243715/109‑1 (MQ=255)
                                                                                                                       atatTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGtttt                                           >  1:1243715/1‑109 (MQ=255)
                                                                                                                         attatCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAg           >  2:22609/1‑139 (MQ=255)
                                                                                                                              cGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGACCtg      <  1:635370/139‑1 (MQ=255)
                                                                                                                              cGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGACCtg      <  1:663838/139‑1 (MQ=255)
                                                                                                                                aaaaGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGACCtgct    >  2:378822/1‑139 (MQ=255)
                                                                                                                                aaaaGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGACCtgct    <  2:107079/139‑1 (MQ=255)
                                                                                                                                  aaGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGACCtgcttg  >  1:713693/1‑139 (MQ=255)
                                                                                                                                  aaGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGACCtgc     >  2:1170179/1‑136 (MQ=255)
                                                                                                                                  aaGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGACCtgc     <  1:1170179/136‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                    
ATCTATTTTGTTTTCATATGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAA‑CCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTCTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGACCTGCTTG  >  NC_000913/2784394‑2784661

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A